Variant report

Variant	rs4646484
Chromosome Location	chr1:47278662-47278663
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:47278520-47278670	GM12872	blood:	n/a	chr1:47278531-47278540

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47274872..47277380-chr1:47277423..47279681,2	K562	blood:
2	chr1:47270918..47272980-chr1:47278589..47280565,2	K562	blood:

Variant related genes	Relation type
CYP4B1	TF binding region
ENSG00000142973	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493125	0.92[EUR][1000 genomes]
rs11211370	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211375	0.81[ASN][1000 genomes]
rs11211376	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211377	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12142787	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12733133	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12742610	0.81[ASN][1000 genomes]
rs2297809	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297810	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297811	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35191195	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35333582	0.95[EUR][1000 genomes]
rs35947953	0.84[ASN][1000 genomes]
rs3766194	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4646480	0.98[EUR][1000 genomes]
rs4646481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4646483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646491	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56101164	0.88[EUR][1000 genomes]
rs590582	0.82[YRI][hapmap]
rs632133	0.82[YRI][hapmap]
rs634431	0.82[YRI][hapmap]
rs6658037	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66871510	0.86[ASN][1000 genomes]
rs6700251	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72681937	0.82[ASN][1000 genomes]
rs7535312	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs837401	0.82[YRI][hapmap]
rs837402	0.82[YRI][hapmap]
rs837403	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004143	chr1:47270942-47321982	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1004246	chr1:47274901-47321982	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv947111	chr1:47277189-47308420	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4646484	BEND5	cis	cerebellum	SCAN
rs4646484	CYP4B1	cis	cerebellum	SCAN
rs4646484	PRDX1	cis	parietal	SCAN
rs4646484	UROD	cis	cerebellum	SCAN
rs4646484	FOXE3	cis	parietal	SCAN
rs4646484	DMAP1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47265600-47279200	Weak transcription	Gastric	stomach
2	chr1:47273400-47285600	Weak transcription	Spleen	Spleen
3	chr1:47277000-47286800	Strong transcription	Esophagus	oesophagus
4	chr1:47278000-47278800	Genic enhancers	Adipose Nuclei	Adipose
5	chr1:47278200-47278800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:47278200-47279400	Genic enhancers	Left Ventricle	heart
7	chr1:47278400-47279200	Weak transcription	Lung	lung
8	chr1:47278600-47279400	Weak transcription	Right Ventricle	heart

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